Uncertainty about Syria's fate is jangling nerves across the Middle East as events conspire to threaten violence and instability far beyond the country's borders.

Israel's swift accusation that Hezbollah and Iran were behind the suicide bombing of a tourist bus in Bulgaria on Wednesday was a stark reminder of a separate but closely related battle between the two most powerful states in the region: Iran's nuclear programme, Israel's alleged assassination of Iranian scientists, and Tehran's close alliance with Damascus make for a dangerous and volatile combination.

The accusation by Syrian state media that the Gulf state of Qatar is faking scenes of mayhem in Damascus was evidence of the belief – whether delusion or propaganda – that President Bashar al-Assad is facing a sinister Arab-western conspiracy to overthrow him, rather than a popular uprising in the spirit of the Arab spring.

It has seemed obvious for some time that Assad's days are numbered, as the rebellion has gathered strength and diplomacy has foundered on divisions between the west and Russia. But even after the sensational assassination of three of his closest security chiefs it is no clearer how much longer he can survive – and what the human cost will be before he goes.

The risks of spillover are growing. Turkey, Lebanon and Jordan worry about refugees streaming across their borders. Jordan is especially concerned about inflows of more Palestinians, who could tip its own fragile ethnic balance. It also fears the growing influence of its own Muslim Brotherhood if Assad is toppled.

Israel, the undisputed and nuclear-armed regional superpower, is concerned about a possible diversionary attack on the Golan Heights, though its military intelligence chief noted this week that Assad has moved troops away from there to protect Damascus.

It also fears the theft of – or accidental damage to – Syria's chemical warfare arsenal. In the worst case it fears such weapons could be transferred to Hezbollah in Lebanon or fall into the hands of jihadi-type groups.

Other alarming scenarios involve acts of desperation by a regime in its death throes. Hezbollah, armed and financed by Iran and helped by Syria, has thousands of rockets it could use to attack deep inside Israel, though the lesson of the 2006 war is that Israel would not hesitate to lay waste to Lebanon in response.

Hassan Nasrallah, the Hezbollah leader, made clear his support for Assad, and on the sixth anniversary of the last war he warned of a "big surprise" if Israel dared to strike. Nasrallah also praised the dead Syrian generals, describing them as "comrades in arms to the resistance and comrades in the [struggle] against the enemy".

No surprise, however, that Ehud Barak, Israel's defence minister, sounded so pleased with what he described as the severe blow suffered by the "radical axis" of Assad, Nasrallah and Mahmoud Ahmadinejad of Iran. Dispelling any doubt, Binyamin Netanyahu, the prime minister, called Iran "the no 1 exporter of terror in the world".

Beyond any immediate risks, Syria's neighbours also worry about what will happen next. The fragmented nature of the anti-Assad opposition does not inspire confidence. The Syrian National Council may be tainted by too close an association with the west, Qatar and the Saudis, and the dominance within it of the Muslim Brotherhood. It is also unclear whether it can impose its will on the Free Syrian Army, let alone on radical smaller groups with a radical agenda.

It is hard to imagine any negotiations between the regime and its enemies while Assad and his inner circle remain in power. That remains the centrepiece of UN envoy Kofi Annan's near moribund peace plan – the only way to de-escalate the crisis. It suffered another perhaps fatal blow at the UN on Thursday.

Further afield, Iran is naturally concerned about the loss of its closest Arab ally – a relationship that dates back to the 1979 revolution. Tehran has flatly denied that it was involved in the killing of five Israeli tourists in Bulgaria. Still, its fingerprints have been easily visible in recent attacks on Israeli targets in Georgia, India and Thailand. Its relationship with Hezbollah is a source or pride. It has reason to believe that its scientists have been murdered by Israel's agents. Israel may decide to make do with a political response. If it takes revenge it will be adding fuel to a highly combustible regional mixture.

Chemical weapons fears

Alarm bells are ringing over Syria's chemical weapons arsenal, believed to be the biggest in the Middle East, because of fears it could be damaged in battle or fall into the hands of terrorists taking advantage of the weakening grip of the Assad regime.

Jordan is also said to have been involved in plans to seize Syrian chemical weapons facilities if the situation deteriorates further. King Abdullah said there was a risk they could be seized by al-Qaida. "We are obviously trying to look for a political solution … if some of those chemical stockpiles were to fall into unfriendly hands," he told CNN.

Syria's arsenal includes mustard gas and deadly nerve agents such as Tabun, Sarin and VX.

Claims by a senior defector that Assad would use them to fight rebels have been treated with scepticism, not least because of echoes of the 2003 Iraq war, when Saddam Hussein's weapons of mass destruction (the ostensible justification for the US-led invasion) turned out to be non-existent.

Neither Syria nor Israel – which has a large but undeclared nuclear arsenal – have signed the international treaty banning chemical weapons.